[ensembl-dev] Codon called wrong in VEP when using custom build cache
Will McLaren
wm2 at ebi.ac.uk
Wed Mar 27 12:26:20 GMT 2013
Thanks Heidi.
I'll look into changing the version of BioPerl that the installer fetches.
Will
On 27 March 2013 12:05, Heidi Viitaniemi <hmviit at utu.fi> wrote:
> Hi Will,
>
> Just as a follow up, the problem was the old version of the bioperl which
> is in the INSTALL.pl.
> Re-installing VEP with a link to pointing to a newer version of bioperl
> did result to the same output with my custom cache asyou got with your run.
>
> Thanks for all your help,
> Heidi
>
> 27.3.2013 8:53, Heidi Viitaniemi kirjoitti:
>
> Hi Will,
>
> And thank you very much for looking into this.
>
> The reason why I want to build my own cahce from gtf and fasta of the
> Gasterosteus_aculeatus is that on groupXIX the two last (of the three )
> supercontigs are flipped in the Ensembl genome (Ross&Peichel 2008). I also
> first thougt that reverse complementing the fasta and gtf for groupXIX was
> the problem but ENSGACG00000003129 is located on a reagion that I didn't
> touch in the gtf or the fasta.
>
> I'll check the versions of Bioperl in our server and try using only the
> fasta and gtf for ENSGACG00000003129.
>
> Thanks,
> Heidi
>
>
> 26.3.2013 16:04, Will McLaren kirjoitti:
>
> Hi Heidi,
>
> Thanks for your patience, I've had a chance to look at this now.
>
> If I build a cache file from the following files:
>
>
> ftp://ftp.ensembl.org/pub/release-70/gtf/gasterosteus_aculeatus/Gasterosteus_aculeatus.BROADS1.70.gtf.gz
>
> and
>
>
> ftp://ftp.ensembl.org/pub/release-70/fasta/gasterosteus_aculeatus/dna/Gasterosteus_aculeatus.BROADS1.70.dna.toplevel.fa.gz
>
> I get (I think!) the correct output from the VEP:
>
> perl gtf2vep.pl -i Gasterosteus_aculeatus.BROADS1.70.gtf.gz -fasta
> Gasterosteus_aculeatus.BROADS1.70.dna.toplevel.fa -species
> gasterosteus_aculeatus -dir test/ -db 70
> perl variant_effect_predictor.pl -i gastero_in.txt -species
> gasterosteus_aculeatus -force -off -dir test/ -db 70
> grep -v # variant_effect_output.txt
>
> groupXIX_2822477_C/T groupXIX:2822477 T
> ENSGACG00000003129 ENSGACT00000004109 Transcript
> missense_variant 67 49 17 A/T Gcg/Acg -
> groupXIX_2822500_T/C groupXIX:2822500 C ENSGACG00000003129
> ENSGACT00000004109 Transcript missense_variant 44 26
> 9 D/G gAc/gGc -
> groupXIX_2822523_C/T groupXIX:2822523 T ENSGACG00000003129
> ENSGACT00000004109 Transcript initiator_codon_variant 21
> 3 1 M/I atG/atA -
> groupXIX_2822541_T/A groupXIX:2822541 A ENSGACG00000003129
> ENSGACT00000004109 Transcript 5_prime_UTR_variant
> 3 - - - - -
>
> This works the same if I use the version 67 files as it appears you have.
>
> So I suspect there is something different about your FASTA file - you
> could check that the sequence of the groupXIX file matches that in the file
> I link to above (do an md5sum or some such thing).
>
> It is also possible that an issue with older versions of BioPerl is to
> blame - there was a known bug in the way BioPerl indexes large FASTA file.
> Normally for Ensembl we recommend using BioPerl 1.2.3 (which contains the
> bug), but VEP works fine with the latest version. I'd try updating your
> BioPerl install to the latest version, remove the *.fa.index file that is
> generated next to your .fa file, and try re-running gtf2vep.pl
>
> Beyond this it's hard to say what's happening without seeing the
> contents of your GTF and FASTA files. If the problem persists, perhaps you
> could just pull out the lines in the GTF for ENSGACT00000004109 and the
> sequence for groupXIX and if that still gives you the same problem, send
> them to me so I can debug.
>
> Hope this helps!
>
> Will
>
>
> On 19 March 2013 12:07, Heidi Viitaniemi <hmviit at utu.fi> wrote:
>
>> Hi Will,
>>
>> And thank you for your response. I'll wait for the solution. I like the
>> idea that you can incorporate your own data to run VEP.
>>
>> Thanks,
>> Heidi Viitaniemi
>>
>>
>>
>> 19.3.2013 13:42, Will McLaren kirjoitti:
>>
>> Hello Heidi,
>>
>> Thanks for finding this - the causes of this bug are I believe somewhat
>> complex so may take a while to get to the bottom of it.
>>
>> Just wanted to let you know that your mail is not being ignored!
>>
>> Regards
>>
>> Will McLaren
>> Ensembl Variation
>>
>>
>> On 18 March 2013 13:48, Heidi Viitaniemi <hmviit at utu.fi> wrote:
>>
>>> Hi,
>>>
>>> I'm running version 2.7 on a unix server. I want to create a custom
>>> cache using my own gtf and fasta with gtf2vep.pl. This works without
>>> problem and also running VEP seems to go fine. The problem is that, in the
>>> output it seems that the cDNA_position, CDS_position and Protein_position
>>> are correct given my input gtf file but the calls for Amino_acids and
>>> Codons seem completely random. If I run against the cache retrieved from
>>> ensembl these are all correct. The version of the genome didn't have an
>>> effect on the output, the gtf's haven't changed. The gtf and the fasta that
>>> I'm using for the custom originate from the ensembl reference so I don't
>>> see any reason why the custom cache shouldn't perform the same way as the
>>> reference from ensembl cache. Could there be bug that somehow messes up the
>>> link between the custom gtf and fasta in my run? Below are the commands I
>>> ran and a snippet of the output's I got.
>>>
>>> Thanks,
>>> Heidi Viitaniemi
>>>
>>> For custom cache I'm running (wrong output for Amino_acids and Codons)
>>> perl gtf2vep.pl -i GasAcu1.67_group_xixflip.gtf -f
>>> gasAcu_group_withoutbac_inv7.fa -d 67 -s
>>> Gasterosteus_aculeatus_XIXflipped_18032013
>>> perl variant_effect_predictor.pl -offline 1 -dir $HOME/.vep -i
>>> ens_realigned_AK_F.var.vcf -format vcf -fork 4 -db_version 67 -species
>>> Gasterosteus_aculeatus_XIXflipped_18032013 -numbers -per_gene -buffer_size
>>> 10000 -o VEP_18032013_exon_pergene_AK_F.var.vcf.txt
>>>
>>> groupXIX_2822477_C/T groupXIX:2822477 T ENSGACG00000003129
>>> ENSGACT00000004109 Transcript missense_variant 67 49 17 G/R Gga/Aga -
>>> EXON=1/2 groupXIX_2822500_T/C groupXIX:2822500 C ENSGACG00000003129
>>> ENSGACT00000004109 Transcript missense_variant 44 26 9 Y/C tAt/tGt -
>>> EXON=1/2 groupXIX_2822523_C/T groupXIX:2822523 T ENSGACG00000003129
>>> ENSGACT00000004109 Transcript synonymous_variant 21 3 1 R cgG/cgA -
>>> EXON=1/2 groupXIX_2822541_T/A groupXIX:2822541 A ENSGACG00000003129
>>> ENSGACT00000004109 Transcript 5_prime_UTR_variant 3 - - - - - EXON=1/2
>>>
>>> For ensembl cache I'm running (correct output for Amino_acids and Codons)
>>> perl variant_effect_predictor.pl -offline -dir $HOME/.vep -i
>>> ens_realigned_AK_F.var.vcf -format vcf -fork 4 -db_version 69 -species
>>> gasterosteus_aculeatus -numbers -per_gene -buffer_size 10000 -o
>>> ensVEP_18032013_exon_pergene_AK_F.var.vcf.txt
>>>
>>> groupXIX_2822477_C/T groupXIX:2822477 T ENSGACG00000003129
>>> ENSGACT00000004109 Transcript missense_variant 67 49 17 A/T Gcg/Acg -
>>> EXON=1/2 groupXIX_2822500_T/C groupXIX:2822500 C ENSGACG00000003129
>>> ENSGACT00000004109 Transcript missense_variant 44 26 9 D/G gAc/gGc -
>>> EXON=1/2 groupXIX_2822523_C/T groupXIX:2822523 T ENSGACG00000003129
>>> ENSGACT00000004109 Transcript initiator_codon_variant 21 3 1 M/I atG/atA
>>> - EXON=1/2 groupXIX_2822541_T/A groupXIX:2822541 A ENSGACG00000003129
>>> ENSGACT00000004109 Transcript 5_prime_UTR_variant 3 - - - - - EXON=1/2
>>>
>>> --
>>> ______________________________________________
>>>
>>> Heidi Viitaniemi
>>> PhD student
>>> Division of Genetics and Physiology
>>> Department of Biology
>>> Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
>>> University of Turku
>>> 20520 Turku
>>>
>>> FINLAND
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
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>>>
>>
>>
>> _______________________________________________
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>>
>>
>> --
>> ______________________________________________
>>
>> Heidi Viitaniemi
>> PhD student
>> Division of Genetics and Physiology
>> Department of Biology
>> Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
>> University of Turku
>> 20520 Turku
>>
>> FINLAND
>>
>>
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
>
> _______________________________________________
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>
>
> --
> ______________________________________________
>
> Heidi Viitaniemi
> PhD student
> Division of Genetics and Physiology
> Department of Biology
> Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
> University of Turku
> 20520 Turku
>
> FINLAND
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
> --
> ______________________________________________
>
> Heidi Viitaniemi
> PhD student
> Division of Genetics and Physiology
> Department of Biology
> Itäinen Pitkäkatu 4A, 7th floor (Pharmacity)
> University of Turku
> 20520 Turku
>
> FINLAND
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
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